Basic corrections & templates
1- It would be nice to get basic corrections (brightness/contrast/saturation/white balance) + lens distortion correction directly in Media Encoder, without needing to create a project in Premiere Pro.
2- It would be nice to be able to save the above settings as templates to be quickly reused
Example use case: I often use Media Encoder to stitch clips from GoPro cameras to get a single video file & reduce file size. Sometimes I would like to add basic corrections to fix brightness and lens distortion (reduce fisheye). It can easily be done in Premiere Pro but it would be so much more convenient and quick to be able to apply the settings directly in Media Encoder and to be able to save/reuse those settings.

